Coexpression cluster:C3045

Full id: C3045_occipital_brain_hippocampus_medial_cerebellum_temporal_amygdala

Phase1 CAGE Peaks

Hg19::chr10:75255724..75255792,-	p1@PPP3CB
Hg19::chr2:86790580..86790591,-	p4@CHMP3 p4@RNF103-CHMP3
Hg19::chr5:171433662..171433686,-	p2@FBXW11

Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

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No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

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GO ID	GO name	FDR corrected p-value
GO:0005955	calcineurin complex	0.0134222261032357
GO:0008287	protein serine/threonine phosphatase complex	0.03969244056313
GO:0004722	protein serine/threonine phosphatase activity	0.03969244056313
GO:0016567	protein ubiquitination	0.03969244056313
GO:0043687	post-translational protein modification	0.03969244056313
GO:0032446	protein modification by small protein conjugation	0.03969244056313
GO:0000151	ubiquitin ligase complex	0.03969244056313
GO:0006464	protein modification process	0.03969244056313
GO:0043412	biopolymer modification	0.03969244056313
GO:0043234	protein complex	0.03969244056313
GO:0005516	calmodulin binding	0.03969244056313
GO:0016055	Wnt receptor signaling pathway	0.03969244056313
GO:0004842	ubiquitin-protein ligase activity	0.03969244056313
GO:0008639	small protein conjugating enzyme activity	0.03969244056313
GO:0032991	macromolecular complex	0.0485798812421496
GO:0019787	small conjugating protein ligase activity	0.0485798812421496
GO:0006470	protein amino acid dephosphorylation	0.0485798812421496

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	2.02e-29	115
neural tube	4.17e-29	57
neural rod	4.17e-29	57
future spinal cord	4.17e-29	57
neural keel	4.17e-29	57
central nervous system	3.25e-25	82
regional part of brain	4.66e-25	59
regional part of nervous system	4.98e-25	94
nervous system	4.98e-25	94
brain	1.44e-23	69
future brain	1.44e-23	69
neural plate	3.48e-23	86
presumptive neural plate	3.48e-23	86
neurectoderm	3.51e-23	90
anterior neural tube	1.92e-22	42
regional part of forebrain	4.72e-22	41
forebrain	4.72e-22	41
future forebrain	4.72e-22	41
gray matter	1.50e-18	34
brain grey matter	1.50e-18	34
ectoderm	1.93e-18	173
presumptive ectoderm	1.93e-18	173
telencephalon	2.48e-18	34
ectoderm-derived structure	3.65e-18	169
regional part of telencephalon	9.61e-18	33
cerebral hemisphere	1.36e-17	32
head	7.94e-17	123
anterior region of body	1.66e-16	129
craniocervical region	1.66e-16	129
pre-chordal neural plate	4.49e-16	61
organism subdivision	1.20e-15	365
regional part of cerebral cortex	2.61e-15	22
neocortex	5.10e-14	20
tube	6.50e-14	194
cerebral cortex	2.05e-13	25
pallium	2.05e-13	25
anatomical conduit	3.51e-13	241
anatomical cluster	2.78e-11	286
multi-tissue structure	1.01e-10	347
cell layer	1.23e-10	312
epithelium	1.42e-10	309
posterior neural tube	8.23e-08	15
chordal neural plate	8.23e-08	15
multi-cellular organism	3.85e-07	659
basal ganglion	8.05e-07	9
nuclear complex of neuraxis	8.05e-07	9
aggregate regional part of brain	8.05e-07	9
collection of basal ganglia	8.05e-07	9
cerebral subcortex	8.05e-07	9
organ part	9.09e-07	219

Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

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Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

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No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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This analysis result is provided for C0 - C305 clusters.